SequenceTubeMap-Sapelo2 - Revision history

Shtsai at 01:33, 5 April 2026

2026-04-05T01:33:38Z

← Older revision		Revision as of 21:33, 4 April 2026
Line 1:		Line 1:
	[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==
	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==
	Sapelo2		Sapelo2

	=== Version ===		== Version ==
	20230906		20230906

	=== Author / Distributor ===		== Author / Distributor ==
	'''[https://vgteam.github.io/ vgteam]'''		'''[https://vgteam.github.io/ vgteam]'''

	=== Description ===		== Description ==
	''"A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg."''		''"A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg."''

	=== Running Program ===		== Running Program ==
	This program, like others, should '''not''' be run on a submit node (''ss-sub2, ss-sub3, ss-sub4, etc''.). Instead, <u>run this program from within an interactive session</u>, which can be entered using the following command on a submit node:<syntaxhighlight lang="bash">		This program, like others, should '''not''' be run on a submit node (''ss-sub2, ss-sub3, ss-sub4, etc''.). Instead, <u>run this program from within an interactive session</u>, which can be entered using the following command on a submit node:<syntaxhighlight lang="bash">
	interact		interact
	</syntaxhighlight>		</syntaxhighlight>

	==== Load Module ====		=== Load Module ===
	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	module load sequenceTubeMap/20230906-GCCcore-11.3.0		module load sequenceTubeMap/20230906-GCCcore-11.3.0
	</syntaxhighlight>		</syntaxhighlight>
	==== Obtain IP Address ====		=== Obtain IP Address ===
	Obtain the IP address of the server that will host '''sequenceTubeMap''' for use in a later step:<syntaxhighlight lang="bash">		Obtain the IP address of the server that will host '''sequenceTubeMap''' for use in a later step:<syntaxhighlight lang="bash">
	hostname -i		hostname -i
	</syntaxhighlight>		</syntaxhighlight>

	==== Starting the server ====		=== Starting the server ===
	Starting the program is as simple as defining the port and data path in environment variables and running the server. '''Make sure to provide the <u>absolute path</u> of your data.'''<syntaxhighlight lang="bash">		Starting the program is as simple as defining the port and data path in environment variables and running the server. '''Make sure to provide the <u>absolute path</u> of your data.'''<syntaxhighlight lang="bash">
	export SERVER_PORT=<port>; export MOUNTED_DATA_PATH=<data_path>; sequenceTubeMap		export SERVER_PORT=<port>; export MOUNTED_DATA_PATH=<data_path>; sequenceTubeMap
	</syntaxhighlight>		</syntaxhighlight>

	==== Configure SSH Tunnel ====		=== Configure SSH Tunnel ===
	It will be necessary to use SSH tunneling to connect to the web frontend from within a web browser. Please note that '''this step is to be performed on your local computer'''. It is recommended to setup the SSH tunnel from a new, separate terminal.		It will be necessary to use SSH tunneling to connect to the web frontend from within a web browser. Please note that '''this step is to be performed on your local computer'''. It is recommended to setup the SSH tunnel from a new, separate terminal.

	'''<u>Note:</u>''' Successfully creating an SSH tunnel at the command line may cause the terminal to seem as though it froze or hung with no response, which is the expected behavior.		'''<u>Note:</u>''' Successfully creating an SSH tunnel at the command line may cause the terminal to seem as though it froze or hung with no response, which is the expected behavior.

	===== SSH Tunneling from Mac or Linux =====		==== SSH Tunneling from Mac or Linux ====
	From your local terminal, issue the following command while making sure to replace '''HOST''' with the actual IP address obtained in the previous step, '''PORT''' with the port number used, and '''MyID''' with your UGA MyID:<syntaxhighlight lang="bash">		From your local terminal, issue the following command while making sure to replace '''HOST''' with the actual IP address obtained in the previous step, '''PORT''' with the port number used, and '''MyID''' with your UGA MyID:<syntaxhighlight lang="bash">
	ssh -N -L PORT:HOST:PORT MyID@sapelo2.gacrc.uga.edu		ssh -N -L PORT:HOST:PORT MyID@sapelo2.gacrc.uga.edu
	</syntaxhighlight>		</syntaxhighlight>

	===== SSH Tunneling from Windows =====		==== SSH Tunneling from Windows ====

	Download the '''[https://the.earth.li/~sgtatham/putty/latest/x86/plink.exe plink program]''', open a command window--the current directory of this command window should contain the ''plink.exe'' file--and execute the following command, replacing '''HOST''' with the actual IP address obtained in the previous step, '''PORT''' with the port number used, and '''MyID''' with your UGA MyID:<syntaxhighlight lang="powershell">		Download the '''[https://the.earth.li/~sgtatham/putty/latest/x86/plink.exe plink program]''', open a command window--the current directory of this command window should contain the ''plink.exe'' file--and execute the following command, replacing '''HOST''' with the actual IP address obtained in the previous step, '''PORT''' with the port number used, and '''MyID''' with your UGA MyID:<syntaxhighlight lang="powershell">
Line 50:		Line 50:
	</syntaxhighlight>		</syntaxhighlight>

	==== Connecting to the Server ====		=== Connecting to the Server ===
	To connect to the server, simply open a web browser <u>on the computer connected to the SSH tunnel</u>, and navigate to [http://localhost:3000 http://localhost:PORT] in the URL bar, making sure to replace PORT with the actual port number used.		To connect to the server, simply open a web browser <u>on the computer connected to the SSH tunnel</u>, and navigate to [http://localhost:3000 http://localhost:PORT] in the URL bar, making sure to replace PORT with the actual port number used.

	=== Example Usage ===		== Example Usage ==

	If the user, ''itd72797'', would like to host this program to visualize his data, he would first enter into an interactive session:<syntaxhighlight lang="bash">		If the user, ''itd72797'', would like to host this program to visualize his data, he would first enter into an interactive session:<syntaxhighlight lang="bash">
Line 67:		Line 67:
	</syntaxhighlight>To connect, he would open a browser window on his personal computer and navigate to http://localhost:8972 .		</syntaxhighlight>To connect, he would open a browser window on his personal computer and navigate to http://localhost:8972 .

	=== Documentation ===		== Documentation ==
	Please reference the program's GitHub page at https://github.com/vgteam/sequenceTubeMap for further reading.		Please reference the program's GitHub page at https://github.com/vgteam/sequenceTubeMap for further reading.

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Isaiah: Made a note that SSH tunneling may cause the terminal to appear frozen.

2023-09-08T14:13:43Z

Made a note that SSH tunneling may cause the terminal to appear frozen.

← Older revision		Revision as of 10:13, 8 September 2023
Line 36:		Line 36:
	==== Configure SSH Tunnel ====		==== Configure SSH Tunnel ====
	It will be necessary to use SSH tunneling to connect to the web frontend from within a web browser. Please note that '''this step is to be performed on your local computer'''. It is recommended to setup the SSH tunnel from a new, separate terminal.		It will be necessary to use SSH tunneling to connect to the web frontend from within a web browser. Please note that '''this step is to be performed on your local computer'''. It is recommended to setup the SSH tunnel from a new, separate terminal.

			'''<u>Note:</u>''' Successfully creating an SSH tunnel at the command line may cause the terminal to seem as though it froze or hung with no response, which is the expected behavior.

	===== SSH Tunneling from Mac or Linux =====		===== SSH Tunneling from Mac or Linux =====

Isaiah at 14:15, 7 September 2023

2023-09-07T14:15:31Z

← Older revision		Revision as of 10:15, 7 September 2023
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			[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		=== Category ===
	Bioinformatics		Bioinformatics

Isaiah: Grammar changes.

2023-09-07T13:43:02Z

Grammar changes.

← Older revision		Revision as of 09:43, 7 September 2023
Line 15:		Line 15:

	=== Running Program ===		=== Running Program ===
	This program, like ~~other~~ should '''not''' be run on a submit node (''ss-sub2, ss-sub3, ss-sub4, etc''). Instead, <u>run this program from within an interactive session</u>, which can be entered using the following command on a submit node:<syntaxhighlight lang="bash">		This program, like others, should '''not''' be run on a submit node (''ss-sub2, ss-sub3, ss-sub4, etc''.). Instead, <u>run this program from within an interactive session</u>, which can be entered using the following command on a submit node:<syntaxhighlight lang="bash">
	interact		interact
	</syntaxhighlight>		</syntaxhighlight>
Line 29:		Line 29:

	==== Starting the server ====		==== Starting the server ====
	Starting the program is as simple as ~~setting the environment variables that define~~ the port and data ~~to,~~ and running the server. '''Make sure to ~~pass~~ the <u>absolute path</u> to your data.'''<syntaxhighlight lang="bash">		Starting the program is as simple as defining the port and data path in environment variables and running the server. '''Make sure to provide the <u>absolute path</u> of your data.'''<syntaxhighlight lang="bash">
	export SERVER_PORT=<port>; export MOUNTED_DATA_PATH=<data_path>; sequenceTubeMap		export SERVER_PORT=<port>; export MOUNTED_DATA_PATH=<data_path>; sequenceTubeMap
	</syntaxhighlight>		</syntaxhighlight>
Line 37:		Line 37:

	===== SSH Tunneling from Mac or Linux =====		===== SSH Tunneling from Mac or Linux =====
	From your local terminal, issue the following command while making sure to replace '''HOST''' with the actual IP address obtained in the previous step and '''MyID''' with your ~~actual~~ MyID:<syntaxhighlight lang="bash">		From your local terminal, issue the following command while making sure to replace '''HOST''' with the actual IP address obtained in the previous step, '''PORT''' with the port number used, and '''MyID''' with your UGA MyID:<syntaxhighlight lang="bash">
	ssh -N -L PORT:HOST:PORT MyID@sapelo2.gacrc.uga.edu		ssh -N -L PORT:HOST:PORT MyID@sapelo2.gacrc.uga.edu
	</syntaxhighlight>		</syntaxhighlight>
Line 43:		Line 43:
	===== SSH Tunneling from Windows =====		===== SSH Tunneling from Windows =====

	Download the '''[https://the.earth.li/~sgtatham/putty/latest/x86/plink.exe plink program]''', open a command window--the current directory of this command window should contain the ''plink.exe'' file--and execute the following command, replacing '''HOST''' with the actual IP address obtained in the previous step and '''MyID''' with your ~~actual~~ MyID:<syntaxhighlight lang="powershell">		Download the '''[https://the.earth.li/~sgtatham/putty/latest/x86/plink.exe plink program]''', open a command window--the current directory of this command window should contain the ''plink.exe'' file--and execute the following command, replacing '''HOST''' with the actual IP address obtained in the previous step, '''PORT''' with the port number used, and '''MyID''' with your UGA MyID:<syntaxhighlight lang="powershell">
	plink -ssh -N -L PORT:HOST:PORT MyID@sapelo2.gacrc.uga.edu		plink -ssh -N -L PORT:HOST:PORT MyID@sapelo2.gacrc.uga.edu
	</syntaxhighlight>		</syntaxhighlight>

	==== Connecting to the Server ====		==== Connecting to the Server ====
	To connect to the server, simply open a web browser <u>on the computer connected to the SSH tunnel</u>, and navigate to [http://localhost:3000 http://localhost:PORT] in the URL bar, ~~'''~~making sure to replace PORT with the actual port number used~~'''~~.		To connect to the server, simply open a web browser <u>on the computer connected to the SSH tunnel</u>, and navigate to [http://localhost:3000 http://localhost:PORT] in the URL bar, making sure to replace PORT with the actual port number used.

	=== Example Usage ===		=== Example Usage ===
Line 58:		Line 58:
	</syntaxhighlight>Third, he would take note of the IP address of the server on which his interactive session is currently running:<syntaxhighlight lang="bash">		</syntaxhighlight>Third, he would take note of the IP address of the server on which his interactive session is currently running:<syntaxhighlight lang="bash">
	hostname -i		hostname -i
	</syntaxhighlight>If he has data in a directory at the file path, ''/home/itd72797/testData'', and would like to host it on port ''8972'', he would execute the following from within the same interactive session:<syntaxhighlight lang="bash">		</syntaxhighlight>If he has data in a directory at the file path ''/home/itd72797/testData'' and would like to host it on port ''8972'', he would execute the following from within the same interactive session:<syntaxhighlight lang="bash">
	export SERVER_PORT=8972; export MOUNTED_DATA_PATH="/home/itd72797/testData"; sequenceTubeMap		export SERVER_PORT=8972; export MOUNTED_DATA_PATH="/home/itd72797/testData"; sequenceTubeMap
	</syntaxhighlight>He would then set up an SSH tunnel by issuing the following from a separate terminal <u>'''on his personal computer'''</u> using the IP address he identified earlier:<syntaxhighlight lang="bash">		</syntaxhighlight>He would then set up an SSH tunnel by issuing the following from a separate terminal <u>'''on his personal computer'''</u> using the IP address he identified earlier, the desired port, and his UGA MyID:<syntaxhighlight lang="bash">
	ssh -N -L 8972:10.33.30.130:8972 itd72797@sapelo2.gacrc.uga.edu		ssh -N -L 8972:10.33.30.130:8972 itd72797@sapelo2.gacrc.uga.edu
	</syntaxhighlight>To connect, he would open a browser window on his personal computer and navigate to http://localhost:8972 .		</syntaxhighlight>To connect, he would open a browser window on his personal computer and navigate to http://localhost:8972 .

Isaiah: Changed "Example Usage" section from "Sub-heading 2" to "Sub-heading 1".

2023-09-07T13:28:53Z

Changed "Example Usage" section from "Sub-heading 2" to "Sub-heading 1".

← Older revision		Revision as of 09:28, 7 September 2023
Line 50:		Line 50:
	To connect to the server, simply open a web browser <u>on the computer connected to the SSH tunnel</u>, and navigate to [http://localhost:3000 http://localhost:PORT] in the URL bar, '''making sure to replace PORT with the actual port number used'''.		To connect to the server, simply open a web browser <u>on the computer connected to the SSH tunnel</u>, and navigate to [http://localhost:3000 http://localhost:PORT] in the URL bar, '''making sure to replace PORT with the actual port number used'''.

	==== Example Usage ====		=== Example Usage ===

	If the user, ''itd72797'', would like to host this program to visualize his data, he would first enter into an interactive session:<syntaxhighlight lang="bash">		If the user, ''itd72797'', would like to host this program to visualize his data, he would first enter into an interactive session:<syntaxhighlight lang="bash">
	interact		interact

Isaiah: Instead of documenting how to set up the program, this page now simply shows how to use the already set up program.

2023-09-07T13:27:35Z

Instead of documenting how to set up the program, this page now simply shows how to use the already set up program.

Show changes

Isaiah: Isaiah moved page SequenceTubeMap to SequenceTubeMap-Sapelo2: Fix name

2023-09-05T17:45:42Z

Isaiah moved page SequenceTubeMap to SequenceTubeMap-Sapelo2: Fix name

← Older revision	Revision as of 13:45, 5 September 2023
(No difference)

Isaiah: Initial creation of page

2023-09-05T17:38:18Z

Initial creation of page

New page

=== Category ===
Bioinformatics

=== Program On ===
[https://github.com/vgteam/sequenceTubeMap GitHub]

=== Version ===
N/A

=== Author / Distributor ===
'''[https://vgteam.github.io/ vgteam]'''

=== Description ===
''"A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg."''

=== Running Program ===

==== Initial Setup ====
Before a user can run this program, it first needs to be setup in a directory of the user's choosing such as the home or scratch directory.

===== Enter Interactive Job =====
This program should be run from within an '''interactive job''', which can be started by issuing the following from a login node:<syntaxhighlight lang="bash">
interact
</syntaxhighlight>

===== Load Dependent Modules =====
As of September 5th, 2023, the dependencies for this program are '''NodeJS''', '''NPM''', and '''vg'''. The '''NPM''' program is included in our '''NodeJS''' module, so the only modules necessary are '''NodeJS''' and '''vg''', which can be loaded with the following:

'''NodeJS'''<syntaxhighlight lang="bash">
module load nodejs/18.12.1-GCCcore-11.3.0
</syntaxhighlight>'''vg'''<syntaxhighlight lang="bash">
module load vg/1.50.1
</syntaxhighlight>

===== Clone Repository =====
From within the directory that will serve to contain this project, clone the '''sequenceTubeMap''' repository:<syntaxhighlight lang="bash">
git clone https://github.com/vgteam/sequenceTubeMap.git
</syntaxhighlight>

===== Install NPM dependencies =====
This program depends on a few other programs from '''NPM'''. To install them, first enter into the '''sequenceTubeMap''' directory that was created when the repository was cloned in the previous step:<syntaxhighlight lang="bash">
cd sequenceTubeMap
</syntaxhighlight>Then, use '''NPM''' to install the additional programs into the project's directory:<syntaxhighlight lang="bash">
npm install
</syntaxhighlight>

===== Build the Frontend =====
Once the additional dependencies have been installed with '''NPM''', '''sequenceTubeMap''' will need to be built:<syntaxhighlight lang="bash">
npm run build
</syntaxhighlight>

==== Starting the server ====
As long as the previous steps have been completed, the program can be started and used when needed. Starting the program is as simple as navigating to the directory in which it is located, and running the server.

===== Enter Interactive Job =====
Unless already in an interactive job, it is necessary to enter into one before loading the modules and starting the server:<syntaxhighlight lang="bash">
interact
</syntaxhighlight>

===== Load Dependent Modules =====
The same versions of the modules that were loaded when performing the initial setup for '''sequenceTubeMap''' should be loaded whenever attempting to run the software:

'''NodeJS'''<syntaxhighlight lang="bash">
module load nodejs/18.12.1-GCCcore-11.3.0
</syntaxhighlight>'''vg'''<syntaxhighlight lang="bash">
module load vg/1.50.1
</syntaxhighlight>

===== Navigate to sequenceTubeMap =====
Unless already in the '''sequenceTubeMap''' directory, change to the location of that directory:<syntaxhighlight lang="bash">
cd /path/to/sequenceTubeMap
</syntaxhighlight>

===== Obtain IP Address =====
Obtain the IP address of the server that will host '''sequenceTubeMap''' for use in the next step:<syntaxhighlight lang="bash">
hostname -i
</syntaxhighlight>

===== Configure SSH Tunnel =====
It will be necessary to use SSH tunneling to connect to the web frontend from within a web browser. Please note that '''this step is to be performed on your local computer'''. It is recommended to setup the SSH tunnel from a new, separate terminal. Currently, the program is hard-coded to run on port 3000, but this can be changed by editing a few files as demonstrated later on this page.

====== SSH Tunneling from Mac or Linux ======
From your local terminal, issue the following command while making sure to replace '''HOST''' with the actual IP address obtained in the previous step and '''MyID''' with your actual MyID:<syntaxhighlight lang="bash">
ssh -N -L 3000:HOST:3000 MyID@sapelo2.gacrc.uga.edu
</syntaxhighlight>

====== SSH Tunneling from Windows ======
Download the '''[https://the.earth.li/~sgtatham/putty/latest/x86/plink.exe plink program]''', open a command window--the current directory of this command window should contain the ''plink.exe'' file--and execute the following command, replacing '''HOST''' with the actual IP address obtained in the previous step and '''MyID''' with your actual MyID:<syntaxhighlight lang="powershell">
plink -ssh -N -L 3000:HOST:3000 MyID@sapelo2.gacrc.uga.edu
</syntaxhighlight>

===== Launch the Program =====
To start the program, return to the terminal in which the interactive session is running, and execute the following command from within the '''sequenceTubeMap''' directory:<syntaxhighlight lang="bash">
npm run serve
</syntaxhighlight>

==== Connecting to the Server ====
To connect to the server, simply open a web browser on the computer connected to the SSH tunnel, and navigate to http://localhost:3000 in the URL bar.

=== Running Program on Different Port ===
As of September 5th, 2023 '''sequenceTubeMap''' is hard-coded to run on port 3000. As a result, using an alternative port number will require manually changing a few files.

The following commands, if issued from within the '''sequenceTubeMap''' directory, will change the necessary files to use port 8942 instead:<syntaxhighlight lang="bash">
sed -i "s/3000/8942/g" server.mjs
sed -i "s/3000/8942/g" setupProxy.js
sed -i "s/3000/8942/g" util/demo-data.js
</syntaxhighlight>If a port is used other than port 3000, use the same number when setting up SSH tunneling:<syntaxhighlight lang="bash">
ssh -N -L 8942:HOST:8942 MyID@sapelo2.gacrc.uga.edu
</syntaxhighlight>Make sure to connect to the correct corresponding port number, http://localhost:8942, when connecting from a web browser as well.

=== Documentation ===
Please reference the program's GitHub page at https://github.com/vgteam/sequenceTubeMap for further reading.

=== System ===
64-bit Linux